CDH3 p.Ala790=
c.2370G>A · rs533035937 · VCV1156330
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -0.99 |
| Overall | ||
| CADD | 8.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0223%
East Asian · 10/44,888 alleles
Filtering AF
0.012%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00916%
Overall
0.00136%
22/1,614,198 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0223% | 4,489 |
| Middle Eastern | 0.0165% | 6,062 |
| African / African-American | 0.00266% | 37,533 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
| European (non-Finnish) | 0.000678% | 147,502 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CDH3
- Protein
- p.Ala790=
- Coding
- c.2370G>A
- MANE Select
- NM_004933 · reported on NM_001793
- dbSNP
- rs533035937
- Type
- single nucleotide variant
- Location
- chr16:68698280 (GRCh38)
- Structure
- AlphaFold pLDDT 78.70
Similar variants
- CDH15 p.Ala790Val Conflicting classifications of pathogenicity ★ ⚠ same residue
- CDH3 p.Ala790Pro Uncertain significance ★ ⚠ same residue
- CDH3 p.Ala790Thr Uncertain significance ★ ⚠ same residue
- CDH3 c.1796-2A>G Pathogenic ★★ same type
- CDH3 c.691+1G>A Pathogenic/Likely pathogenic ★★ same type
- CDH3 p.Arg103Ter Pathogenic ★★ same type
- CDH3 p.Arg221Ter Pathogenic ★★ same type
- CDH3 p.Arg503His Pathogenic/Likely pathogenic ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cdh3-p-ala790 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown